treatment of gap characters

The matrix itself may well contain gap characters after alignment. The analysis isn't reproducible if you don't know how these gaps were treated in the tree inference stage, and the effects between different treatments can often be non-trivial. The treatment can't be inferred simply from looking at the matrix or software used in most cases.

If it's judged not "important enough" then fine. But I thought I'd propose it here anyhow. 

Has it been been discussed for inclusion before? Apologies if it has.